Fighters attacked the offices of a powerful Shia party in at least five cities, setting many of them ablaze.
In a separate incident on Wednesday in Mosul to the north, armed men raided an Iraqi police checkpoint on Wednesday and killed five policemen and a civilian, police said.
Al-Maliki, in a statement on Wednesday, said: "The situation in Karbala is under control after military reinforcements arrived and police and military special forces have spread throughout the city to purge those killers and criminals."
Sporadic and occasionally sustained gunfire could still be heard after dawn in the city, coming from the area around the shrines of Imam Hussein and Imam Abbas.
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The fighting killed 52 people and wounded 206 on Tuesday, a senior security official in Baghdad said.
The general director of the al-Hussein hospital in Karbala, 110km south of the capital, said it had received 34 bodies and treated 239 wounded.
Ali Kadhum, an official at the shrines' media office, said the two shrines had been slightly damaged, with bullets hitting their domes and minarets and an electric power station ruined.
Hundreds of thousands of pilgrims had gathered in the city to mark the birthday of the 12th and last Shia imam.
The interior ministry accused al-Mahdi army, a militia loyal to Muqtada al-Sadr, the Shia leader, of attacking government forces in Karbala, the site of two shrines under the control of the Supreme Iraqi Islamic Council (SIIC).
Al-Sadr's forces are vying with the SIIC for power in the regions south of Baghdad.
Al-Sadr called for calm on Tuesday night but police said SIIC buildings were torched overnight in Baghdad's Kadhimiya neighbourhood, in the city of Kufa, in Iskandariya and in al-Hamza district of Babil province.
Another SIIC headquarters was struck by rocket-propelled grenades in the centre of Najaf.